#2078 closed enhancement (fixed)

R module lwgeom

Reported by: darkblueb Owned by: osgeolive@…
Priority: normal Milestone: OSGeoLive12.0
Component: OSGeoLive Keywords: R, sf
Cc: edzer

Description

12dev alpha1 ; install R lwgeom. Q. does not find GEOS make_valid() ?

user@osgeolive:~$ sudo su - -c "R -e \"install.packages('lwgeom', repos='http://cran.rstudio.com/')\""

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> install.packages('lwgeom', repos='http://cran.rstudio.com/')
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/lwgeom_0.1-4.tar.gz'
Content type 'application/x-gzip' length 432706 bytes (422 KB)
==================================================
downloaded 422 KB

* installing *source* package ‘lwgeom’ ...
** package ‘lwgeom’ successfully unpacked and MD5 sums checked
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: pkg-config proj exists, will use it
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
configure: PROJ: 4.9.3
checking for pj_init_plus in -lproj... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
checking for geos-config... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.6.2
checking GEOS version >= 3.3.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib/x86_64-linux-gnu -lgeos_c... yes
checking for lwgeom_make_valid in -llwgeom... no
checking for pj_init_plus in -lproj... (cached) yes
checking for GEOS_init_r in -lgeos_c... yes
checking liblwgeom_internal.h usability... no
checking liblwgeom_internal.h presence... no
checking for liblwgeom_internal.h... no
configure: Package CPP flags:  -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H
configure: Package LIBS:  -lproj -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geodetic.cpp -o geodetic.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lwgeom.cpp -o lwgeom.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c proj.cpp -o proj.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geos.cpp -o geos.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.cpp -o io.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/box2d.c -o liblwgeom/box2d.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/bytebuffer.c -o liblwgeom/bytebuffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/effectivearea.c -o liblwgeom/effectivearea.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/g_box.c -o liblwgeom/g_box.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/g_serialized.c -o liblwgeom/g_serialized.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/g_util.c -o liblwgeom/g_util.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/kmeans.c -o liblwgeom/kmeans.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwalgorithm.c -o liblwgeom/lwalgorithm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwboundingcircle.c -o liblwgeom/lwboundingcircle.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwcircstring.c -o liblwgeom/lwcircstring.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwcollection.c -o liblwgeom/lwcollection.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwcompound.c -o liblwgeom/lwcompound.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwcurvepoly.c -o liblwgeom/lwcurvepoly.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeodetic.c -o liblwgeom/lwgeodetic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeodetic_tree.c -o liblwgeom/lwgeodetic_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_api.c -o liblwgeom/lwgeom_api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom.c -o liblwgeom/lwgeom.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_debug.c -o liblwgeom/lwgeom_debug.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_geos.c -o liblwgeom/lwgeom_geos.o
liblwgeom/lwgeom_geos.c: In function ‘LWGEOM2GEOS’:
liblwgeom/lwgeom_geos.c:381:12: warning: statement will never be executed [-Wswitch-unreachable]
   LWPOINT *lwp = NULL;
            ^~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_geos_clean.c -o liblwgeom/lwgeom_geos_clean.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_geos_cluster.c -o liblwgeom/lwgeom_geos_cluster.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_geos_node.c -o liblwgeom/lwgeom_geos_node.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_geos_split.c -o liblwgeom/lwgeom_geos_split.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_median.c -o liblwgeom/lwgeom_median.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_topo.c -o liblwgeom/lwgeom_topo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_transform.c -o liblwgeom/lwgeom_transform.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwgeom_wrapx.c -o liblwgeom/lwgeom_wrapx.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwhomogenize.c -o liblwgeom/lwhomogenize.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_encoded_polyline.c -o liblwgeom/lwin_encoded_polyline.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_geojson.c -o liblwgeom/lwin_geojson.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_twkb.c -o liblwgeom/lwin_twkb.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_wkb.c -o liblwgeom/lwin_wkb.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwiterator.c -o liblwgeom/lwiterator.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwkmeans.c -o liblwgeom/lwkmeans.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwlinearreferencing.c -o liblwgeom/lwlinearreferencing.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwline.c -o liblwgeom/lwline.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwmcurve.c -o liblwgeom/lwmcurve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwmline.c -o liblwgeom/lwmline.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwmpoint.c -o liblwgeom/lwmpoint.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwmpoly.c -o liblwgeom/lwmpoly.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwmsurface.c -o liblwgeom/lwmsurface.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_encoded_polyline.c -o liblwgeom/lwout_encoded_polyline.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_geojson.c -o liblwgeom/lwout_geojson.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_gml.c -o liblwgeom/lwout_gml.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_kml.c -o liblwgeom/lwout_kml.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_svg.c -o liblwgeom/lwout_svg.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_twkb.c -o liblwgeom/lwout_twkb.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_wkb.c -o liblwgeom/lwout_wkb.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_x3d.c -o liblwgeom/lwout_x3d.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwpoint.c -o liblwgeom/lwpoint.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwpoly.c -o liblwgeom/lwpoly.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwprint.c -o liblwgeom/lwprint.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwpsurface.c -o liblwgeom/lwpsurface.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwspheroid.c -o liblwgeom/lwspheroid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwstroke.c -o liblwgeom/lwstroke.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwtin.c -o liblwgeom/lwtin.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwtree.c -o liblwgeom/lwtree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwtriangle.c -o liblwgeom/lwtriangle.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwunionfind.c -o liblwgeom/lwunionfind.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwutil.c -o liblwgeom/lwutil.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/measures3d.c -o liblwgeom/measures3d.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/measures.c -o liblwgeom/measures.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/ptarray.c -o liblwgeom/ptarray.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/stringbuffer.c -o liblwgeom/stringbuffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/varint.c -o liblwgeom/varint.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_wkt_parse.c -o liblwgeom/lwin_wkt_parse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_wkt_lex.c -o liblwgeom/lwin_wkt_lex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwout_wkt.c -o liblwgeom/lwout_wkt.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPOSTGIS_GEOS_VERSION=35 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/sf/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c liblwgeom/lwin_wkt.c -o liblwgeom/lwin_wkt.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lwgeom.so geodetic.o lwgeom.o RcppExports.o proj.o geos.o io.o liblwgeom/box2d.o liblwgeom/bytebuffer.o liblwgeom/effectivearea.o liblwgeom/g_box.o liblwgeom/g_serialized.o liblwgeom/g_util.o liblwgeom/kmeans.o liblwgeom/lwalgorithm.o liblwgeom/lwboundingcircle.o liblwgeom/lwcircstring.o liblwgeom/lwcollection.o liblwgeom/lwcompound.o liblwgeom/lwcurvepoly.o liblwgeom/lwgeodetic.o liblwgeom/lwgeodetic_tree.o liblwgeom/lwgeom_api.o liblwgeom/lwgeom.o liblwgeom/lwgeom_debug.o liblwgeom/lwgeom_geos.o liblwgeom/lwgeom_geos_clean.o liblwgeom/lwgeom_geos_cluster.o liblwgeom/lwgeom_geos_node.o liblwgeom/lwgeom_geos_split.o liblwgeom/lwgeom_median.o liblwgeom/lwgeom_topo.o liblwgeom/lwgeom_transform.o liblwgeom/lwgeom_wrapx.o liblwgeom/lwhomogenize.o liblwgeom/lwin_encoded_polyline.o liblwgeom/lwin_geojson.o liblwgeom/lwin_twkb.o liblwgeom/lwin_wkb.o liblwgeom/lwiterator.o liblwgeom/lwkmeans.o liblwgeom/lwlinearreferencing.o liblwgeom/lwline.o liblwgeom/lwmcurve.o liblwgeom/lwmline.o liblwgeom/lwmpoint.o liblwgeom/lwmpoly.o liblwgeom/lwmsurface.o liblwgeom/lwout_encoded_polyline.o liblwgeom/lwout_geojson.o liblwgeom/lwout_gml.o liblwgeom/lwout_kml.o liblwgeom/lwout_svg.o liblwgeom/lwout_twkb.o liblwgeom/lwout_wkb.o liblwgeom/lwout_x3d.o liblwgeom/lwpoint.o liblwgeom/lwpoly.o liblwgeom/lwprint.o liblwgeom/lwpsurface.o liblwgeom/lwspheroid.o liblwgeom/lwstroke.o liblwgeom/lwtin.o liblwgeom/lwtree.o liblwgeom/lwtriangle.o liblwgeom/lwunionfind.o liblwgeom/lwutil.o liblwgeom/measures3d.o liblwgeom/measures.o liblwgeom/ptarray.o liblwgeom/stringbuffer.o liblwgeom/varint.o liblwgeom/lwin_wkt_parse.o liblwgeom/lwin_wkt_lex.o liblwgeom/lwout_wkt.o liblwgeom/lwin_wkt.o -lproj -lgeos_c -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/lwgeom/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (lwgeom)

The downloaded source packages are in
	‘/tmp/RtmpkHyGqa/downloaded_packages’
> 
> 
user@osgeolive:~$ R

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library('lwgeom')
Linking to liblwgeom 2.5.0dev r16016, GEOS 3.6.2, proj.4 4.9.3
> help(lwgeom)
No documentation for ‘lwgeom’ in specified packages and libraries:
you could try ‘??lwgeom’
> ??legeom
> lwgeom::lwgeom_extSoftVersion
function () 
{
    structure(c(CPL_lwgeom_version(), CPL_geos_version(), CPL_proj_version()), 
        names = c("lwgeom", "GEOS", "proj.4"))
}
<environment: namespace:lwgeom>
> lwgeom::lwgeom_extSoftVersion()
           lwgeom              GEOS            proj.4 
"2.5.0dev r16016"           "3.6.2"           "4.9.3" 
> 
> 
Save workspace image? [y/n/c]: n

Change history (4)

comment:1 Changed 17 months ago by edzer

GEOS doesn't have a make_valid. The test that sais "no" checks for liblwgeom to be available on the system. It doesn't find it, and continues to compile its own version; nothing unexpected; try

example(st_make_valid)

after loading lwgeom to check it is there.

comment:2 Changed 16 months ago by darkblueb

12dev branch notebooktest

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
....

> library('lwgeom')
Linking to liblwgeom 2.5.0dev r16016, GEOS 3.6.2, proj.4 4.9.3
> example(st_make_valid) 

st_mk_> library(sf)
Linking to GEOS 3.6.2, GDAL 2.2.3, proj.4 4.9.3

st_mk_> x = st_sfc(st_polygon(list(rbind(c(0,0),c(0.5,0),c(0.5,0.5),c(0.5,0),c(1,0),c(1,1),c(0,1),c(0,0)))))

st_mk_> suppressWarnings(st_is_valid(x))
[1] FALSE

st_mk_> y = lwgeom::st_make_valid(x)

st_mk_> st_is_valid(y)
[1] TRUE

st_mk_> y %>% st_cast()
Geometry set for 2 features 
geometry type:  GEOMETRY
dimension:      XY
bbox:           xmin: 0 ymin: 0 xmax: 1 ymax: 1
epsg (SRID):    NA
proj4string:    NA
POLYGON ((0.5 0, 0 0, 0 1, 1 1, 1 0, 0.5 0))
LINESTRING (0.5 0, 0.5 0.5)

Last edited 16 months ago by darkblueb (previous) (diff)

comment:3 Changed 15 months ago by bakaniko

Available in OSGeoLive 12.0b2

Closing ticket. Thanks Brian

comment:4 Changed 15 months ago by bakaniko

Resolution: fixed
Status: assignedclosed
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